This paper describes the simulation of a methanol spray flame in the NIST reference spray combustion facility, which was predicted using a state-of-the-art, unstructured-mesh CFD code. The code solves the gas-phase equations in an Eulerian frame using the finite-volume approach while the droplet equations are solved in a Lagrangian frame. This paper focuses on the sensitivity of the predicted flame structure to the model boundary conditions, to ensure matching of the simulation to the experimental conditions. The combustor uses a simplex pressure-jet atomizer to produce a hollow-cone spray with a cone angle of 60°. The overall equivalence ratio of the baseline operating condition is 0.29. The spray initial conditions are specified from the measurement data obtained close to the atomizer. For this case, several simulations were performed with different initial and boundary conditions. The parameters that were varied from the baseline case included the air swirl velocity, equivalence ratio, spray droplet size distribution, and a pre-exponential kinetic constant. The results indicate that the existence of a central recirculation zone is sensitive to the location and rate of heat release. The predicted flame structure appears to be in reasonable agreement with NIST flame visualization. The fuel conversion is predicted to be 100 % whereas the data indicates a conversion of 80 %. This discrepancy is attributed to the uncertainty in spray initial conditions, especially for the droplet size distribution.